This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 79 arm-level results and 5 clinical features across 454 patients, 55 significant findings detected with Q value < 0.25.
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5p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.
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13q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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17p gain cnv correlated to 'Time to Death'.
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18p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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19p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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19q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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3p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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7p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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7q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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8p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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8q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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9p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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9q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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11p loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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11q loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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12p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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12q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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14q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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15q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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16p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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16q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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17p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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17q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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18q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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19q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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21q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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22q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
11p loss | 0 (0%) | 405 |
0.000531 (0.181) |
7.91e-05 (0.0279) |
5.69e-08 (2.16e-05) |
0.32 (1.00) |
0.541 (1.00) |
11q loss | 0 (0%) | 413 |
0.000143 (0.0499) |
8.79e-05 (0.0309) |
3.51e-07 (0.000131) |
0.155 (1.00) |
0.0814 (1.00) |
5p gain | 0 (0%) | 425 |
2.57e-05 (0.00932) |
0.108 (1.00) |
1.48e-06 (0.000547) |
0.674 (1.00) |
0.0573 (1.00) |
13q gain | 0 (0%) | 434 |
0.399 (1.00) |
0.000471 (0.162) |
5.35e-06 (0.00197) |
0.618 (1.00) |
0.172 (1.00) |
18p gain | 0 (0%) | 420 |
0.129 (1.00) |
0.000385 (0.133) |
6.24e-09 (2.37e-06) |
0.558 (1.00) |
0.0318 (1.00) |
19p gain | 0 (0%) | 428 |
0.0734 (1.00) |
2.84e-05 (0.0103) |
0.000133 (0.0467) |
0.276 (1.00) |
0.0982 (1.00) |
19q gain | 0 (0%) | 431 |
0.00816 (1.00) |
6.14e-06 (0.00225) |
2.49e-07 (9.31e-05) |
0.64 (1.00) |
0.18 (1.00) |
8p loss | 0 (0%) | 410 |
0.351 (1.00) |
3.38e-05 (0.0121) |
3.51e-18 (1.38e-15) |
0.73 (1.00) |
0.594 (1.00) |
9p loss | 0 (0%) | 387 |
0.696 (1.00) |
3.32e-06 (0.00122) |
5.64e-15 (2.2e-12) |
0.885 (1.00) |
0.177 (1.00) |
9q loss | 0 (0%) | 371 |
0.211 (1.00) |
3.71e-10 (1.43e-07) |
1.73e-12 (6.7e-10) |
0.595 (1.00) |
0.67 (1.00) |
14q loss | 0 (0%) | 416 |
0.342 (1.00) |
0.000169 (0.059) |
4.4e-09 (1.68e-06) |
0.853 (1.00) |
0.0762 (1.00) |
15q loss | 0 (0%) | 385 |
0.619 (1.00) |
2.91e-05 (0.0105) |
7.77e-13 (3.03e-10) |
0.252 (1.00) |
0.919 (1.00) |
16p loss | 0 (0%) | 395 |
0.0166 (1.00) |
3.3e-05 (0.0118) |
7.87e-10 (3.02e-07) |
0.76 (1.00) |
0.0339 (1.00) |
16q loss | 0 (0%) | 357 |
0.0229 (1.00) |
9.45e-07 (0.00035) |
1.24e-15 (4.84e-13) |
0.261 (1.00) |
0.0416 (1.00) |
17p loss | 0 (0%) | 364 |
0.124 (1.00) |
6.58e-07 (0.000245) |
8.68e-22 (3.42e-19) |
0.439 (1.00) |
0.126 (1.00) |
17q loss | 0 (0%) | 393 |
0.815 (1.00) |
0.000264 (0.0914) |
9.97e-08 (3.75e-05) |
0.174 (1.00) |
0.207 (1.00) |
22q loss | 0 (0%) | 378 |
0.00403 (1.00) |
0.000369 (0.128) |
5.95e-10 (2.29e-07) |
0.27 (1.00) |
0.67 (1.00) |
17p gain | 0 (0%) | 448 |
0.000521 (0.178) |
0.762 (1.00) |
0.477 (1.00) |
0.367 (1.00) |
0.0755 (1.00) |
20p gain | 0 (0%) | 398 |
0.0072 (1.00) |
0.00239 (0.787) |
6.56e-08 (2.47e-05) |
0.0187 (1.00) |
0.0744 (1.00) |
20q gain | 0 (0%) | 388 |
0.0423 (1.00) |
0.00265 (0.868) |
8.67e-13 (3.37e-10) |
0.013 (1.00) |
0.0205 (1.00) |
21q gain | 0 (0%) | 432 |
0.85 (1.00) |
0.00279 (0.911) |
7.27e-05 (0.0257) |
1 (1.00) |
0.773 (1.00) |
3p loss | 0 (0%) | 427 |
0.122 (1.00) |
0.00974 (1.00) |
5.79e-05 (0.0206) |
0.829 (1.00) |
0.792 (1.00) |
4p loss | 0 (0%) | 402 |
0.0411 (1.00) |
0.000759 (0.257) |
1.15e-12 (4.48e-10) |
0.196 (1.00) |
0.0746 (1.00) |
4q loss | 0 (0%) | 405 |
0.0273 (1.00) |
0.00544 (1.00) |
1.3e-09 (5e-07) |
0.0318 (1.00) |
0.501 (1.00) |
5p loss | 0 (0%) | 433 |
0.327 (1.00) |
0.911 (1.00) |
2.87e-05 (0.0104) |
0.807 (1.00) |
0.153 (1.00) |
5q loss | 0 (0%) | 419 |
0.8 (1.00) |
0.0219 (1.00) |
6.11e-09 (2.33e-06) |
0.336 (1.00) |
0.187 (1.00) |
7p loss | 0 (0%) | 429 |
0.352 (1.00) |
0.0113 (1.00) |
0.000262 (0.0911) |
1 (1.00) |
0.255 (1.00) |
7q loss | 0 (0%) | 431 |
0.848 (1.00) |
0.00105 (0.355) |
6.37e-08 (2.41e-05) |
1 (1.00) |
0.287 (1.00) |
8q loss | 0 (0%) | 447 |
0.689 (1.00) |
0.62 (1.00) |
1.53e-05 (0.00558) |
0.679 (1.00) |
0.228 (1.00) |
12p loss | 0 (0%) | 433 |
0.422 (1.00) |
0.00817 (1.00) |
1.33e-06 (0.00049) |
0.633 (1.00) |
0.873 (1.00) |
12q loss | 0 (0%) | 441 |
0.447 (1.00) |
0.0157 (1.00) |
0.000482 (0.165) |
1 (1.00) |
1 (1.00) |
13q loss | 0 (0%) | 402 |
0.137 (1.00) |
0.00167 (0.559) |
0.000477 (0.163) |
0.52 (1.00) |
0.545 (1.00) |
18q loss | 0 (0%) | 412 |
0.505 (1.00) |
0.0433 (1.00) |
7.98e-06 (0.00291) |
0.287 (1.00) |
0.16 (1.00) |
19p loss | 0 (0%) | 424 |
0.345 (1.00) |
0.906 (1.00) |
1.44e-07 (5.39e-05) |
0.837 (1.00) |
0.124 (1.00) |
19q loss | 0 (0%) | 430 |
0.572 (1.00) |
0.99 (1.00) |
3.61e-05 (0.0128) |
1 (1.00) |
0.0808 (1.00) |
21q loss | 0 (0%) | 428 |
0.307 (1.00) |
0.469 (1.00) |
2.92e-05 (0.0105) |
0.375 (1.00) |
0.293 (1.00) |
1p gain | 0 (0%) | 436 |
0.0642 (1.00) |
0.0394 (1.00) |
0.0272 (1.00) |
0.605 (1.00) |
0.85 (1.00) |
1q gain | 0 (0%) | 323 |
0.56 (1.00) |
0.062 (1.00) |
0.000772 (0.261) |
0.496 (1.00) |
0.0784 (1.00) |
2p gain | 0 (0%) | 406 |
0.0921 (1.00) |
0.0363 (1.00) |
0.0609 (1.00) |
0.509 (1.00) |
0.518 (1.00) |
2q gain | 0 (0%) | 416 |
0.111 (1.00) |
0.187 (1.00) |
0.116 (1.00) |
0.463 (1.00) |
0.172 (1.00) |
3p gain | 0 (0%) | 430 |
0.478 (1.00) |
0.428 (1.00) |
0.568 (1.00) |
0.0673 (1.00) |
0.361 (1.00) |
3q gain | 0 (0%) | 411 |
0.0444 (1.00) |
0.176 (1.00) |
0.00168 (0.559) |
0.603 (1.00) |
0.0524 (1.00) |
4p gain | 0 (0%) | 448 |
0.596 (1.00) |
0.00713 (1.00) |
0.00252 (0.829) |
1 (1.00) |
0.677 (1.00) |
5q gain | 0 (0%) | 446 |
0.317 (1.00) |
0.919 (1.00) |
0.0128 (1.00) |
1 (1.00) |
0.0324 (1.00) |
6p gain | 0 (0%) | 420 |
0.685 (1.00) |
0.283 (1.00) |
0.00418 (1.00) |
1 (1.00) |
0.733 (1.00) |
6q gain | 0 (0%) | 425 |
0.975 (1.00) |
0.284 (1.00) |
0.0107 (1.00) |
0.534 (1.00) |
0.673 (1.00) |
7p gain | 0 (0%) | 414 |
0.373 (1.00) |
0.738 (1.00) |
0.17 (1.00) |
0.102 (1.00) |
0.737 (1.00) |
7q gain | 0 (0%) | 416 |
0.0264 (1.00) |
0.585 (1.00) |
0.886 (1.00) |
0.139 (1.00) |
0.48 (1.00) |
8p gain | 0 (0%) | 374 |
0.0017 (0.564) |
0.314 (1.00) |
0.805 (1.00) |
0.589 (1.00) |
0.214 (1.00) |
8q gain | 0 (0%) | 349 |
0.00798 (1.00) |
0.711 (1.00) |
0.0216 (1.00) |
0.715 (1.00) |
0.12 (1.00) |
9p gain | 0 (0%) | 443 |
0.787 (1.00) |
0.774 (1.00) |
0.274 (1.00) |
0.0387 (1.00) |
0.0956 (1.00) |
9q gain | 0 (0%) | 451 |
0.797 (1.00) |
0.775 (1.00) |
0.0495 (1.00) |
0.559 (1.00) |
|
10p gain | 0 (0%) | 372 |
0.667 (1.00) |
0.548 (1.00) |
0.286 (1.00) |
0.894 (1.00) |
0.979 (1.00) |
10q gain | 0 (0%) | 377 |
0.889 (1.00) |
0.718 (1.00) |
0.275 (1.00) |
1 (1.00) |
0.379 (1.00) |
11p gain | 0 (0%) | 448 |
0.448 (1.00) |
0.48 (1.00) |
0.0423 (1.00) |
1 (1.00) |
0.0572 (1.00) |
11q gain | 0 (0%) | 447 |
0.551 (1.00) |
0.526 (1.00) |
0.264 (1.00) |
1 (1.00) |
0.203 (1.00) |
12p gain | 0 (0%) | 421 |
0.534 (1.00) |
0.702 (1.00) |
0.00923 (1.00) |
0.845 (1.00) |
0.498 (1.00) |
12q gain | 0 (0%) | 428 |
0.801 (1.00) |
0.47 (1.00) |
0.455 (1.00) |
0.829 (1.00) |
0.317 (1.00) |
14q gain | 0 (0%) | 437 |
0.2 (1.00) |
0.424 (1.00) |
0.0141 (1.00) |
0.0294 (1.00) |
0.919 (1.00) |
15q gain | 0 (0%) | 449 |
0.00974 (1.00) |
0.503 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.0368 (1.00) |
16p gain | 0 (0%) | 443 |
0.319 (1.00) |
0.131 (1.00) |
0.0191 (1.00) |
0.52 (1.00) |
0.553 (1.00) |
16q gain | 0 (0%) | 450 |
0.671 (1.00) |
0.49 (1.00) |
0.644 (1.00) |
0.325 (1.00) |
0.0184 (1.00) |
17q gain | 0 (0%) | 443 |
0.0904 (1.00) |
0.0815 (1.00) |
0.341 (1.00) |
0.739 (1.00) |
0.067 (1.00) |
18q gain | 0 (0%) | 437 |
0.0121 (1.00) |
0.0375 (1.00) |
0.00139 (0.467) |
0.417 (1.00) |
0.391 (1.00) |
22q gain | 0 (0%) | 447 |
0.507 (1.00) |
0.0248 (1.00) |
0.00622 (1.00) |
1 (1.00) |
0.367 (1.00) |
Xq gain | 0 (0%) | 446 |
0.102 (1.00) |
0.167 (1.00) |
0.0128 (1.00) |
1 (1.00) |
0.496 (1.00) |
1p loss | 0 (0%) | 443 |
0.344 (1.00) |
0.267 (1.00) |
0.0141 (1.00) |
0.314 (1.00) |
0.388 (1.00) |
1q loss | 0 (0%) | 450 |
0.0124 (1.00) |
0.184 (1.00) |
0.0236 (1.00) |
0.325 (1.00) |
0.0787 (1.00) |
2p loss | 0 (0%) | 448 |
0.532 (1.00) |
0.0731 (1.00) |
0.688 (1.00) |
0.186 (1.00) |
0.0526 (1.00) |
2q loss | 0 (0%) | 447 |
0.344 (1.00) |
0.0313 (1.00) |
0.515 (1.00) |
0.111 (1.00) |
0.0946 (1.00) |
3q loss | 0 (0%) | 442 |
0.223 (1.00) |
0.155 (1.00) |
0.0369 (1.00) |
0.523 (1.00) |
0.518 (1.00) |
6p loss | 0 (0%) | 447 |
0.152 (1.00) |
0.173 (1.00) |
0.07 (1.00) |
0.426 (1.00) |
1 (1.00) |
6q loss | 0 (0%) | 445 |
0.51 (1.00) |
0.188 (1.00) |
0.0322 (1.00) |
0.46 (1.00) |
1 (1.00) |
10p loss | 0 (0%) | 437 |
0.0289 (1.00) |
0.0704 (1.00) |
0.00169 (0.561) |
1 (1.00) |
0.28 (1.00) |
10q loss | 0 (0%) | 437 |
0.447 (1.00) |
0.0158 (1.00) |
0.0471 (1.00) |
0.788 (1.00) |
1 (1.00) |
18p loss | 0 (0%) | 425 |
0.221 (1.00) |
0.119 (1.00) |
0.00125 (0.421) |
0.674 (1.00) |
0.0764 (1.00) |
20p loss | 0 (0%) | 441 |
0.574 (1.00) |
0.0847 (1.00) |
0.0233 (1.00) |
0.218 (1.00) |
0.518 (1.00) |
20q loss | 0 (0%) | 448 |
0.48 (1.00) |
0.244 (1.00) |
0.0144 (1.00) |
0.367 (1.00) |
1 (1.00) |
Xq loss | 0 (0%) | 440 |
0.621 (1.00) |
0.105 (1.00) |
0.00858 (1.00) |
0.0753 (1.00) |
0.159 (1.00) |
P value = 2.57e-05 (logrank test), Q value = 0.0093
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 42 | 0.0 - 187.1 (15.5) |
5P GAIN CNV | 29 | 8 | 0.1 - 59.0 (10.9) |
5P GAIN WILD-TYPE | 421 | 34 | 0.0 - 187.1 (15.9) |
P value = 1.48e-06 (Fisher's exact test), Q value = 0.00055
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
5P GAIN CNV | 11 | 1 | 17 |
5P GAIN WILD-TYPE | 340 | 17 | 68 |
P value = 0.000471 (t-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
13Q GAIN CNV | 20 | 69.3 (6.1) |
13Q GAIN WILD-TYPE | 433 | 63.4 (11.4) |
P value = 5.35e-06 (Fisher's exact test), Q value = 0.002
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
13Q GAIN CNV | 6 | 1 | 13 |
13Q GAIN WILD-TYPE | 345 | 17 | 72 |
P value = 0.000521 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 42 | 0.0 - 187.1 (15.5) |
17P GAIN CNV | 6 | 2 | 3.0 - 15.8 (12.1) |
17P GAIN WILD-TYPE | 444 | 40 | 0.0 - 187.1 (15.9) |
P value = 0.000385 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
18P GAIN CNV | 34 | 69.7 (9.4) |
18P GAIN WILD-TYPE | 419 | 63.1 (11.2) |
P value = 6.24e-09 (Fisher's exact test), Q value = 2.4e-06
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
18P GAIN CNV | 11 | 2 | 21 |
18P GAIN WILD-TYPE | 340 | 16 | 64 |
P value = 2.84e-05 (t-test), Q value = 0.01
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
19P GAIN CNV | 26 | 70.9 (7.5) |
19P GAIN WILD-TYPE | 427 | 63.2 (11.3) |
P value = 0.000133 (Fisher's exact test), Q value = 0.047
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
19P GAIN CNV | 12 | 0 | 14 |
19P GAIN WILD-TYPE | 339 | 18 | 71 |
P value = 6.14e-06 (t-test), Q value = 0.0022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
19Q GAIN CNV | 23 | 72.3 (7.5) |
19Q GAIN WILD-TYPE | 430 | 63.2 (11.2) |
P value = 2.49e-07 (Fisher's exact test), Q value = 9.3e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
19Q GAIN CNV | 7 | 0 | 16 |
19Q GAIN WILD-TYPE | 344 | 18 | 69 |
P value = 6.56e-08 (Fisher's exact test), Q value = 2.5e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
20P GAIN CNV | 26 | 3 | 27 |
20P GAIN WILD-TYPE | 325 | 15 | 58 |
P value = 8.67e-13 (Fisher's exact test), Q value = 3.4e-10
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
20Q GAIN CNV | 27 | 3 | 36 |
20Q GAIN WILD-TYPE | 324 | 15 | 49 |
P value = 7.27e-05 (Fisher's exact test), Q value = 0.026
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
21Q GAIN CNV | 9 | 0 | 13 |
21Q GAIN WILD-TYPE | 342 | 18 | 72 |
P value = 5.79e-05 (Fisher's exact test), Q value = 0.021
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
3P LOSS CNV | 11 | 3 | 13 |
3P LOSS WILD-TYPE | 340 | 15 | 72 |
P value = 1.15e-12 (Fisher's exact test), Q value = 4.5e-10
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
4P LOSS CNV | 18 | 3 | 31 |
4P LOSS WILD-TYPE | 333 | 15 | 54 |
P value = 1.3e-09 (Fisher's exact test), Q value = 5e-07
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
4Q LOSS CNV | 19 | 4 | 26 |
4Q LOSS WILD-TYPE | 332 | 14 | 59 |
P value = 2.87e-05 (Fisher's exact test), Q value = 0.01
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
5P LOSS CNV | 8 | 0 | 13 |
5P LOSS WILD-TYPE | 343 | 18 | 72 |
P value = 6.11e-09 (Fisher's exact test), Q value = 2.3e-06
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
5Q LOSS CNV | 12 | 1 | 22 |
5Q LOSS WILD-TYPE | 339 | 17 | 63 |
P value = 0.000262 (Fisher's exact test), Q value = 0.091
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
7P LOSS CNV | 11 | 1 | 13 |
7P LOSS WILD-TYPE | 340 | 17 | 72 |
P value = 6.37e-08 (Fisher's exact test), Q value = 2.4e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
7Q LOSS CNV | 6 | 1 | 16 |
7Q LOSS WILD-TYPE | 345 | 17 | 69 |
P value = 3.38e-05 (t-test), Q value = 0.012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
8P LOSS CNV | 44 | 68.6 (7.4) |
8P LOSS WILD-TYPE | 409 | 63.1 (11.5) |
P value = 3.51e-18 (Fisher's exact test), Q value = 1.4e-15
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
8P LOSS CNV | 9 | 2 | 33 |
8P LOSS WILD-TYPE | 342 | 16 | 52 |
P value = 1.53e-05 (Fisher's exact test), Q value = 0.0056
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
8Q LOSS CNV | 0 | 0 | 7 |
8Q LOSS WILD-TYPE | 351 | 18 | 78 |
P value = 3.32e-06 (t-test), Q value = 0.0012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
9P LOSS CNV | 67 | 68.7 (8.8) |
9P LOSS WILD-TYPE | 386 | 62.8 (11.4) |
P value = 5.64e-15 (Fisher's exact test), Q value = 2.2e-12
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
9P LOSS CNV | 25 | 4 | 38 |
9P LOSS WILD-TYPE | 326 | 14 | 47 |
P value = 3.71e-10 (t-test), Q value = 1.4e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
9Q LOSS CNV | 83 | 69.8 (8.7) |
9Q LOSS WILD-TYPE | 370 | 62.3 (11.3) |
P value = 1.73e-12 (Fisher's exact test), Q value = 6.7e-10
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
9Q LOSS CNV | 38 | 5 | 40 |
9Q LOSS WILD-TYPE | 313 | 13 | 45 |
P value = 0.000531 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 42 | 0.0 - 187.1 (15.5) |
11P LOSS CNV | 48 | 10 | 0.0 - 102.0 (12.1) |
11P LOSS WILD-TYPE | 402 | 32 | 0.0 - 187.1 (16.0) |
P value = 7.91e-05 (t-test), Q value = 0.028
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
11P LOSS CNV | 49 | 69.3 (9.8) |
11P LOSS WILD-TYPE | 404 | 63.0 (11.2) |
P value = 5.69e-08 (Fisher's exact test), Q value = 2.2e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
11P LOSS CNV | 21 | 4 | 24 |
11P LOSS WILD-TYPE | 330 | 14 | 61 |
P value = 0.000143 (logrank test), Q value = 0.05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 450 | 42 | 0.0 - 187.1 (15.5) |
11Q LOSS CNV | 40 | 9 | 0.0 - 102.0 (11.6) |
11Q LOSS WILD-TYPE | 410 | 33 | 0.0 - 187.1 (16.0) |
P value = 8.79e-05 (t-test), Q value = 0.031
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
11Q LOSS CNV | 41 | 69.7 (9.4) |
11Q LOSS WILD-TYPE | 412 | 63.0 (11.2) |
P value = 3.51e-07 (Fisher's exact test), Q value = 0.00013
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
11Q LOSS CNV | 17 | 5 | 19 |
11Q LOSS WILD-TYPE | 334 | 13 | 66 |
P value = 1.33e-06 (Fisher's exact test), Q value = 0.00049
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
12P LOSS CNV | 6 | 1 | 14 |
12P LOSS WILD-TYPE | 345 | 17 | 71 |
P value = 0.000482 (Fisher's exact test), Q value = 0.16
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
12Q LOSS CNV | 4 | 1 | 8 |
12Q LOSS WILD-TYPE | 347 | 17 | 77 |
P value = 0.000477 (Fisher's exact test), Q value = 0.16
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
13Q LOSS CNV | 29 | 3 | 20 |
13Q LOSS WILD-TYPE | 322 | 15 | 65 |
P value = 0.000169 (t-test), Q value = 0.059
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
14Q LOSS CNV | 38 | 69.2 (8.6) |
14Q LOSS WILD-TYPE | 415 | 63.1 (11.3) |
P value = 4.4e-09 (Fisher's exact test), Q value = 1.7e-06
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
14Q LOSS CNV | 13 | 3 | 22 |
14Q LOSS WILD-TYPE | 338 | 15 | 63 |
P value = 2.91e-05 (t-test), Q value = 0.01
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
15Q LOSS CNV | 69 | 68.9 (10.7) |
15Q LOSS WILD-TYPE | 384 | 62.7 (11.1) |
P value = 7.77e-13 (Fisher's exact test), Q value = 3e-10
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
15Q LOSS CNV | 28 | 6 | 35 |
15Q LOSS WILD-TYPE | 323 | 12 | 50 |
P value = 3.3e-05 (t-test), Q value = 0.012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
16P LOSS CNV | 59 | 69.0 (9.8) |
16P LOSS WILD-TYPE | 394 | 62.8 (11.2) |
P value = 7.87e-10 (Fisher's exact test), Q value = 3e-07
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
16P LOSS CNV | 25 | 5 | 29 |
16P LOSS WILD-TYPE | 326 | 13 | 56 |
P value = 9.45e-07 (t-test), Q value = 0.00035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
16Q LOSS CNV | 97 | 68.1 (9.4) |
16Q LOSS WILD-TYPE | 356 | 62.4 (11.4) |
P value = 1.24e-15 (Fisher's exact test), Q value = 4.8e-13
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
16Q LOSS CNV | 44 | 6 | 47 |
16Q LOSS WILD-TYPE | 307 | 12 | 38 |
P value = 6.58e-07 (t-test), Q value = 0.00024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
17P LOSS CNV | 90 | 68.4 (9.4) |
17P LOSS WILD-TYPE | 363 | 62.4 (11.4) |
P value = 8.68e-22 (Fisher's exact test), Q value = 3.4e-19
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
17P LOSS CNV | 33 | 7 | 50 |
17P LOSS WILD-TYPE | 318 | 11 | 35 |
P value = 0.000264 (t-test), Q value = 0.091
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
17Q LOSS CNV | 61 | 68.5 (10.5) |
17Q LOSS WILD-TYPE | 392 | 62.9 (11.2) |
P value = 9.97e-08 (Fisher's exact test), Q value = 3.7e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
17Q LOSS CNV | 29 | 5 | 27 |
17Q LOSS WILD-TYPE | 322 | 13 | 58 |
P value = 7.98e-06 (Fisher's exact test), Q value = 0.0029
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
18Q LOSS CNV | 20 | 6 | 16 |
18Q LOSS WILD-TYPE | 331 | 12 | 69 |
P value = 1.44e-07 (Fisher's exact test), Q value = 5.4e-05
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
19P LOSS CNV | 10 | 2 | 18 |
19P LOSS WILD-TYPE | 341 | 16 | 67 |
P value = 3.61e-05 (Fisher's exact test), Q value = 0.013
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
19Q LOSS CNV | 9 | 2 | 13 |
19Q LOSS WILD-TYPE | 342 | 16 | 72 |
P value = 2.92e-05 (Fisher's exact test), Q value = 0.01
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
21Q LOSS CNV | 10 | 3 | 13 |
21Q LOSS WILD-TYPE | 341 | 15 | 72 |
P value = 0.000369 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 453 | 63.6 (11.2) |
22Q LOSS CNV | 76 | 67.3 (9.0) |
22Q LOSS WILD-TYPE | 377 | 62.9 (11.5) |
P value = 5.95e-10 (Fisher's exact test), Q value = 2.3e-07
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 351 | 18 | 85 |
22Q LOSS CNV | 36 | 6 | 34 |
22Q LOSS WILD-TYPE | 315 | 12 | 51 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = UCEC-TP.clin.merged.picked.txt
-
Number of patients = 454
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 5
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.